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An intronic SNP in a RUNX1 binding site of SLC22A4, encoding an organic cation transporter, is associated with rheumatoid arthritis

Abstract

Rheumatoid arthritis is a common inflammatory disease with complex genetic components. We investigated the genetic contribution of the cytokine gene cluster in chromosome 5q31 to susceptibility to rheumatoid arthritis in the Japanese population by case-control linkage disequilibrium (LD) mapping using single nucleotide polymorphisms (SNPs). Here we report that there is significant association between rheumatoid arthritis and the organic cation transporter gene SLC22A4 (P = 0.000034). We show that expression of SLC22A4 is specific to hematological and immunological tissues and that SLC22A4 is also highly expressed in the inflammatory joints of mice with collagen-induced arthritis. A SNP affects the transcriptional efficiency of SLC22A4 in vitro, owing to an allelic difference in affinity to Runt-related transcription factor 1 (RUNX1), a transcriptional regulator in the hematopoietic system. A SNP in RUNX1 is also strongly associated with rheumatoid arthritis (P = 0.00035). Our data indicate that the regulation of SLC22A4 expression by RUNX1 is associated with susceptibility to rheumatoid arthritis, which may represent an example of an epistatic effect of two genes on this disorder.

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Figure 1: LD blocks and genomic structure of NT_007072.11.
Figure 2: Expression patterns of SLC22A4 and SLC22A5 in human tissues and cells.
Figure 3: EMSAs and supershift assays with DIG-labeled oligonucleotides of 30 bp corresponding to the slc2F2 polymorphic site.
Figure 4: Comparison of allelic variants of slc2F2 analyzed by relative luciferase activity.

References

  1. Seldin, M.F., Amos, C.I., Ward, R. & Gregersen, P.K. The genetics revolution and the assault on rheumatoid arthritis. Arthritis Rheum. 42, 1071–1079 (1999).

    Article  CAS  Google Scholar 

  2. Deighton, C.M., Walker, D.J., Griffiths, I.D. & Roberts, D.F. The contribution of HLA to rheumatoid arthritis. Clin. Genet. 36, 178–182 (1989).

    Article  CAS  Google Scholar 

  3. Nepom, G.T. Major histocompatibility complex-directed susceptibility to rheumatoid arthritis. Adv. Immunol. 68, 315–332 (1998).

    Article  CAS  Google Scholar 

  4. Cornelis, F. et al. New susceptibility locus for rheumatoid arthritis suggested by a genome-wide linkage study. Proc. Natl. Acad. Sci. USA 95, 10746–10750 (1998).

    Article  CAS  Google Scholar 

  5. Jawaheer, D. et al. A genomewide screen in multiplex rheumatoid arthritis families suggests genetic overlap with other autoimmune diseases. Am. J. Hum. Genet. 68, 927–936 (2001).

    Article  CAS  Google Scholar 

  6. MacKay, K. et al. Whole-genome linkage analysis of rheumatoid arthritis susceptibility loci in 252 affected sibling pairs in the United Kingdom. Arthritis Rheum. 46, 632–639 (2002).

    Article  CAS  Google Scholar 

  7. Jawaheer, D. et al. Screening the genome for rheumatoid arthritis susceptibility genes: a replication study and combined analysis of 512 multicase families. Arthritis Rheum. 48, 906–916 (2003).

    Article  CAS  Google Scholar 

  8. Shiozawa, S. et al. Identification of the gene loci that predispose to rheumatoid arthritis. Int. Immunol. 10, 1891–1895 (1998).

    Article  CAS  Google Scholar 

  9. Tabor, H.K., Risch, N.J. & Myers, R.M. Opinion: Candidate-gene approaches for studying complex genetic traits: practical considerations. Nat. Rev. Genet. 3, 391–397 (2002).

    Article  CAS  Google Scholar 

  10. Ardlie, K.G., Kruglyak, L. & Seielstad, M. Patterns of linkage disequilibrium in the human genome. Nat. Rev. Genet. 3, 299–309 (2002).

    Article  CAS  Google Scholar 

  11. Ohnishi, Y. et al. A high-throughput SNP typing system for genome-wide association studies. J. Hum. Genet. 46, 471–477 (2001).

    Article  CAS  Google Scholar 

  12. Ozaki, K. et al. Functional SNPs in the lymphotoxin-α gene that are associated with susceptibility to myocardial infarction. Nat. Genet. 32, 650–654 (2002).

    Article  CAS  Google Scholar 

  13. Suzuki, A. et al. Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis. Nat. Genet. 34, 395–402 (2003).

    Article  CAS  Google Scholar 

  14. Goldbach-Mansky, R. et al. Rheumatoid arthritis associated autoantibodies in patients with synovitis of recent onset. Arthritis Res. 2, 236–243 (2000).

    Article  CAS  Google Scholar 

  15. Grunig, G. et al. Requirement for IL-13 independently of IL-4 in experimental asthma. Science 282, 2261–2263 (1998).

    Article  CAS  Google Scholar 

  16. Rioux, J.D. et al. Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease. Nat. Genet. 29, 223–228 (2001).

    Article  CAS  Google Scholar 

  17. Mansur, A.H., Bishop, D.T., Markham, A.F., Britton, J. & Morrison, J.F. Association study of asthma and atopy traits and chromosome 5q cytokine cluster markers. Clin. Exp. Allergy 28, 141–150 (1998).

    Article  CAS  Google Scholar 

  18. Kauppi, P. et al. A second–generation association study of the 5q31 cytokine gene cluster and the interleukin-4 receptor in asthma. Genomics 77, 35–42 (2001).

    Article  CAS  Google Scholar 

  19. Lee, J.K., Park, C., Kimm, K. & Rutherford, M.S. Genome-wide multilocus analysis for immune-mediated complex diseases. Biochem. Biophys. Res. Commun. 295, 771–773 (2002).

    Article  CAS  Google Scholar 

  20. Lutterbach, B. & Hiebert, S.W. Role of the transcription factor AML-1 in acute leukemia and hematopoietic differentiation. Gene 245, 223–235 (2000).

    Article  CAS  Google Scholar 

  21. Miyoshi, H. et al. t(8;21) breakpoints on chromosome 21 in acute myeloid leukemia are clustered within a limited region of a single gene, AML1. Proc. Natl. Acad. Sci. USA 88, 10431–10434 (1991).

    Article  CAS  Google Scholar 

  22. Prokunina, L. et al. A regulatory polymorphism in PDCD1 is associated with susceptibility to systemic lupus erythematosus in humans. Nat. Genet. 32, 666–669 (2002).

    Article  CAS  Google Scholar 

  23. Haga, H., Yamada, R., Ohnishi, Y., Nakamura, Y. & Tanaka, T. Gene-based SNP discovery as part of the Japanese Millennium Genome Project: identification of 190,562 genetic variations in the human genome. Single-nucleotide polymorphism. J. Hum. Genet. 47, 605–610 (2002).

    Article  CAS  Google Scholar 

  24. Nielsen, D.M., Ehm, M.G. & Weir, B.S. Detecting marker-disease association by testing for Hardy-Weinberg disequilibrium at a marker locus. Am. J. Hum. Genet. 63, 1531–1540 (1998).

    Article  CAS  Google Scholar 

  25. Devlin, B. & Risch, N. A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 29, 311–322 (1995).

    Article  CAS  Google Scholar 

  26. Ott, J. Counting methods (EM algorithm) in human pedigree analysis: linkage and segregation analysis. Ann. Hum. Genet. 40, 443–454 (1977).

    Article  CAS  Google Scholar 

  27. Saito, S. et al. Catalog of 238 variations among six human genes encoding solute carriers (hSLCs) in the Japanese population. J. Hum. Genet. 47, 576–584 (2002).

    Article  CAS  Google Scholar 

  28. Heinemeyer, T. et al. Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res. 26, 362–367 (1998).

    Article  CAS  Google Scholar 

  29. Galson, D.L. & Housman, D.E. Detection of two tissue-specific DNA-binding proteins with affinity for sites in the mouse β-globin intervening sequence 2. Mol. Cell. Biol. 8, 381–392 (1988).

    Article  CAS  Google Scholar 

  30. Pahl, H.L. et al. The proto-oncogene PU.1 regulates expression of the myeloid-specific CD11b promoter. J. Biol. Chem. 268, 5014–5020 (1993).

    CAS  Google Scholar 

  31. Cordell, H.J. Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans. Hum. Mol. Genet 11, 2463–2468 (2002).

    Article  CAS  Google Scholar 

  32. Wu, X. et al. Identity of the organic cation transporter OCT3 as the extraneuronal monoamine transporter (uptake2) and evidence for the expression of the transporter in the brain. J. Biol. Chem. 273, 32776–32786 (1998).

    Article  CAS  Google Scholar 

  33. Yabuuchi, H. et al. Novel membrane transporter OCTN1 mediates multispecific, bidirectional, and pH-dependent transport of organic cations. J. Pharmacol. Exp. Ther. 289, 768–773 (1999).

    CAS  PubMed  Google Scholar 

  34. Motohashi, H. et al. Gene expression levels and immunolocalization of organic ion transporters in the human kidney. J. Am. Soc. Nephrol. 13, 866–874 (2002).

    CAS  PubMed  Google Scholar 

  35. Surinya, K.H., Cox, T.C. & May, B.K. Identification and characterization of a conserved erythroid-specific enhancer located in intron 8 of the human 5-aminolevulinate synthase 2 gene. J. Biol. Chem. 273, 16798–16809 (1998).

    Article  CAS  Google Scholar 

  36. Ghayor, C. et al. Regulation of human COL2A1 gene expression in chondrocytes. Identification of C-Krox-responsive elements and modulation by phenotype alteration. J. Biol. Chem. 275, 27421–27438 (2000).

    CAS  PubMed  Google Scholar 

  37. Beohar, N. & Kawamoto, S. Transcriptional regulation of the human nonmuscle myosin II heavy chain-A gene. Identification of three clustered cis-elements in intron-1 which modulate transcription in a cell type– and differentiation state–dependent manner. J. Biol. Chem. 273, 9168–9178 (1998).

    Article  CAS  Google Scholar 

  38. Uchida, H., Zhang, J. & Nimer, S.D. AML1A and AML1B can transactivate the human IL-3 promoter. J. Immunol. 158, 2251–2258 (1997).

    CAS  PubMed  Google Scholar 

  39. Takahashi, A. et al. Positive and negative regulation of granulocyte-macrophage colony-stimulating factor promoter activity by AML1-related transcription factor, PEBP2. Blood 86, 607–616 (1995).

    CAS  PubMed  Google Scholar 

  40. Olofsson, P. et al. Positional identification of Ncf1 as a gene that regulates arthritis severity in rats. Nat. Genet. 33, 25–32 (2003).

    Article  CAS  Google Scholar 

  41. Arnett, F.C. et al. The American Rheumatism Association 1987 revised criteria for the classification of rheumatoid arthritis. Arthritis Rheum. 31, 315–324 (1988).

    Article  CAS  Google Scholar 

  42. Miyazawa, K., Mori, A., Yamamoto, K. & Okudaira, H. Transcriptional roles of CCAAT/enhancer binding protein-β, nuclear factor-κB, and C-promoter binding factor 1 in interleukin (IL)-1β-induced IL-6 synthesis by human rheumatoid fibroblast-like synoviocytes. J. Biol. Chem. 273, 7620–7627 (1998).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank E. Tatsu, K. Kobayashi, E. Kanno, M. Mito, N. Iwamoto and the other members of the Laboratory for Rheumatic Diseases for technical assistance; H. Kawakami for computer programming; many members of the SNP Research Center for assistance; S. Tsukada, D. Nakai, R. Nakagomi, R. Kawaida and M. Nakayama-Hamada for discussions; and M. Yukioka, S. Tohma, T. Matsubara, S. Wakitani, R. Teshima and Y. Nishioka for clinical sample collection. This work was supported by a grant from the Japanese Millennium Project.

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Correspondence to Ryo Yamada.

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Tokuhiro, S., Yamada, R., Chang, X. et al. An intronic SNP in a RUNX1 binding site of SLC22A4, encoding an organic cation transporter, is associated with rheumatoid arthritis. Nat Genet 35, 341–348 (2003). https://doi.org/10.1038/ng1267

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